Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
PiGenome Resource Report Resource Website |
PiGenome (RRID:SCR_013394) | PiGenome | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Database for ESTs (Expressed Sequence Tags), consensus sequences, bacterial artificial chromosome (BAC) clones, BES (BAC End Sequences). They have generated 69,545 ESTs from 6 full-length cDNA libraries (Porcine Abdominal Fat, Porcine Fat Cell, Porcine Loin Muscle, Liver and Pituitary gland). They have also identified a total of 182 BAC contigs from chromosome 6. It is very valuable resources to study porcine quantitative trait loci (QTL) mapping and genome study. Users can explore genomic alignment of various data types, including expressed sequence tags (ESTs), consensus sequences, singletons, QTL, Marker, UniGene and BAC clones by several options. To estimate the genomic location of sequence dataset, their data aligned BES (BAC End Sequences) instead of genomic sequence because Pig Genome has low-coverage sequencing data. Sus scrofa Genome Database mainly provide comparative map of four species (pig, cattle, dog and mouse) in chromosome 6. | gene expression, genome, sequence, gene, expressed sequence tag, consensus sequence, bac clone, bac end sequence, bac contig, quantitative trait loci, singleton, marker, unigene, chromosome 6, blast, transcript, bacterial artificial chromosome, snp, alignment |
is related to: Gene Ontology has parent organization: National Institute of Animal Science; Gyeonggi-do; South Korea |
National Institute of Animal Science; Gyeonggi-do; Korea ; Korean Rural Development Administration ; Biogreen21 Project 20050301034467 |
PMID:19082661 | nlx_153888 | http://pigenome.nabc.go.kr/ | SCR_013394 | Sus scrofa Genome database, Pig Genome Database, Pigenome database | 2026-09-05 06:27:35 | 0 | |||||
|
ENIGMA Resource Report Resource Website 100+ mentions |
ENIGMA (RRID:SCR_013400) | data analysis software, data processing software, software application, software resource | A software tool to extract gene expression modules from perturbational microarray data, based on the use of combinatorial statistics and graph-based clustering. The modules are further characterized by incorporating other data types, e.g. GO annotation, protein interactions and transcription factor binding information, and by suggesting regulators that might have an effect on the expression of (some of) the genes in the module. Version : ENIGMA 1.1 used GO annotation version : Aug 29th 2007 | genome, gene, genetic software, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Ghent University; Ghent; Belgium is parent organization of: ENIGMA-DTI Pipeline |
PMID:18402676 | biotools:enigma, nlx_144365 | https://bio.tools/enigma | SCR_013400 | 2026-09-05 06:27:35 | 133 | ||||||||
|
Genetic Association Information Network (GAIN) Resource Report Resource Website 1+ mentions |
Genetic Association Information Network (GAIN) (RRID:SCR_013703) | GAIN | consortium, data or information resource, organization portal, portal | The Genetic Association Information Network (GAIN) supports a series of Genome-Wide Association Studies (GWAS) designed to identify specific points of DNA variation associated with the occurrence of a particular common disease. Initially focusing on six major common diseases, GAIN focused on combining the results with clinical data to create a significant new resource for genetic researchers. | tool development, biomarker research, data-sharing enabler, genome, genome wide association studies, FNIH, | has parent organization: Foundation for the National Institutes of Health | Pfizer Inc ; Affymetrix Inc |
SCR_013703 | 2026-09-05 06:27:39 | 9 | |||||||||
|
RAST Server Resource Report Resource Website 1000+ mentions |
RAST Server (RRID:SCR_014606) | RAST | production service resource, service resource | A SEED-quality automated service that annotates complete or nearly complete bacterial and archaeal genomes across the entire phylogenetic tree. RAST can also be used to analyze draft genomes. | microbiome, seed, annotate, genome, bacteria, archaea, service, bio.tools |
is listed by: Human Microbiome Project is listed by: Debian is listed by: bio.tools |
National Science Foundation 0850546; NIAID contract HHSN272200900040C |
PMID:18261238 | Free for the scientific community, Login required | biotools:theseed | https://bio.tools/theseed | SCR_014606 | Rapid Annotation using Subsystem Technology, Rapid Annotation using Subsystem Technology Server | 2026-09-05 06:27:48 | 1198 | ||||
|
Prokka Resource Report Resource Website 1000+ mentions |
Prokka (RRID:SCR_014732) | data analysis software, data processing software, sequence analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for the rapid annotation of prokaryotic genomes. It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank/DDJB/ENA. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | annotation, prokaryote, genome, prokaryotic genome, sequence analysis software, annotation software, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
DOI:10.1093/bioinformatics/btu153 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04220, biotools:prokka | https://bio.tools/prokka, https://sources.debian.org/src/prokka/, https://sources.debian.org/src/prokka/ | SCR_014732 | 2026-09-05 06:27:50 | 4882 | |||||||
|
Encode Resource Report Resource Website 1000+ mentions |
Encode (RRID:SCR_015482) | consortium, data or information resource, data set, organization portal, portal | Consortium to build comprehensive parts list of functional elements in human genome. This includes elements that act at protein and RNA levels, and regulatory elements that control cells and circumstances in which gene is active. Data from 2012-present. | genome, sequencing, protein, rna, dna, consortium |
is related to: modENCODE is related to: ENCODE is related to: 3D Genome has parent organization: Stanford University; Stanford; California has parent organization: University of California at Santa Cruz; California; USA |
NHGRI HG006992 | PMID:15499007 | Free, Freely available | SCR_015482 | ENCODE Project | 2026-09-05 06:27:55 | 1293 | |||||||
|
SwiftOrtho Resource Report Resource Website 1+ mentions |
SwiftOrtho (RRID:SCR_017122) | data analysis software, data processing software, software application, software resource | Software tool for orthology analysis to identify orthologs, paralogs and co orthologs for genomes. Used to perform homology classification across genomes of different species in large genomic datasets. | orthology, analysis, identify, ortholog, paralog, co ortholog, genome, homology, different, species, large, dataset, bio.tools |
uses: Python Programming Language is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1101/543223 | Free, Available for download, Freely available | OMICS_30890, biotools:SwiftOrtho | https://bio.tools/SwiftOrtho | SCR_017122 | 2026-09-05 06:28:19 | 4 | |||||||
|
Flye Resource Report Resource Website 100+ mentions |
Flye (RRID:SCR_017016) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software package as de novo assembler for single molecule sequencing reads. Used for assembling long, error prone reads such as those produced by PacBio and Oxford Nanopore Technologies, for fast and accurate genome reconstructions. Available for Linux and MacOS platforms. | assembler, single, molecule, sequencing, long, error, read, fast, accurate, genome, reconstruction, nucleotide, quality, data, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of California at San Diego; California; USA |
PMID:27956617 | Free, Available for download, Freely available | biotools:Flye | https://bio.tools/Flye, https://sources.debian.org/src/flye/ | SCR_017016 | 2026-09-05 06:28:17 | 324 | |||||||
|
dndSCV Resource Report Resource Website 10+ mentions |
dndSCV (RRID:SCR_017093) | data analysis software, data processing software, software application, software resource | Software R package as suite of dN/dS methods to quantify selection in cancer and somatic evolution. Contains functions to quantify dN/dS ratios for missense, nonsense and essential splice mutations, at level of individual genes, groups of genes or at whole genome level. Used to detect cancer driver genes on datasets. | dN/dS, method, quantify, selection, cancer, somatic, evolution, missense, nonsense, essential, splice, mutation, gene, genome, dataset |
uses: devtools is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_017093 | 2026-09-05 06:28:18 | 36 | ||||||||||
|
RNAmmer Resource Report Resource Website 100+ mentions |
RNAmmer (RRID:SCR_017075) | analysis service resource, data access protocol, data analysis service, data analysis software, data processing software, production service resource, service resource, software application, software resource, standalone software, web service | Software package to predict ribosomal RNA genes in full genome sequences by utilising two levels of Hidden Markov Models. Consistent and rapid annotation of ribosomal RNA genes. | predict, ribosomal, RNA, gene, full, genome, sequence, HMM, rRNA | has parent organization: Technical University of Denmark; Lyngby; Denmark | Danish Center for Scientific Computing ; EMBIO at the University of Oslo ; European Union ; Research Council of Norway |
PMID:17452365 | Restricted | SCR_017075 | 2026-09-05 06:28:18 | 120 | ||||||||
|
Maize Database of Images and Genomes Resource Report Resource Website 1+ mentions |
Maize Database of Images and Genomes (RRID:SCR_016987) | MaizeDIG | analysis service resource, data or information resource, database, production service resource, service resource | Genotype and phenotype database for maize images based on BioDIG. Supports multiple reference genomes and has been integrated with the MaizeGDB Genome Browser to make custom tracks showing mutant phenotypes within their genomic context. Allows for custom tagging of images to highlight regions related to the phenotypes. This is accomplished through an interface allowing users to create links from images to genomic coordinates and to curate and search images by gene model ID, gene symbol, and gene name. | genotype, phenotype, collection, maize, image, reference, genome | works with: MaizeGDB | Free, Freely available | SCR_016987 | Maize Dig, MaizeDatabase of Images and Genomes, MaizeDig, MaizeDIG | 2026-09-05 06:28:16 | 5 | ||||||||
|
WTDBG Resource Report Resource Website 50+ mentions |
WTDBG (RRID:SCR_017225) | alignment software, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource | Software tool as de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies. It assembles raw reads without error correction and then builds consensus from intermediate assembly output. Desiged to assemble huge genomes in very limited time. | sequence, assembler, de novo, long, noisy, read, likelihood, estimator, genome |
is listed by: OMICtools is listed by: Debian |
NHGRI R01 HG010040; NSFC |
PMID:31819265 | Free, Available for download, Freely available | OMICS_24025 | https://github.com/ruanjue/wtdbg, https://sources.debian.org/src/wtdbg2/ | SCR_017225 | Wtdbg2, wtdgb, Wtdgb, wtdgb2 | 2026-09-05 06:28:20 | 66 | |||||
|
3D de novo assembly Resource Report Resource Website 10+ mentions |
3D de novo assembly (RRID:SCR_017227) | data analysis software, data processing software, software application, software resource | Software tool as 3D de novo assembly (3D DNA) pipeline. Used to help generate HI-C assembly. | de novo, assembly, 3D, DNA, HI-C, data, scaffold, pipeline, chromosome, genome | DOI:10.1126/science.aal3327 | Free, Available for download, Freely available | SCR_017227 | 2026-09-05 06:28:20 | 42 | ||||||||||
|
matemaker Resource Report Resource Website 1+ mentions |
matemaker (RRID:SCR_017199) | data analysis software, data processing software, sequence analysis software, software application, software resource, standalone software | Software tool to make artificial mate pairs from long sequences for scaffolding. | artificial, mate, pair, long, sequence, scaffolding, genomics, genome, assembly | Free, Available for download, Freely available | SCR_017199 | matemaker v1.0.0 | 2026-09-05 06:28:20 | 4 | ||||||||||
|
phyloscanner Resource Report Resource Website 1+ mentions |
phyloscanner (RRID:SCR_017400) | data analysis software, data processing software, software application, software resource | Software tool for analysing pathogen genetic diversity and relationships between and within hosts at once, in windows along genome. Inferring transmission from within and between host pathogen genetic diversity. | Analysing, pathogen, genetic, diversity, relationship, host, genome | Bill & Melinda Gates Foundation ; ERC Advanced Grant ; Medical Research Council |
PMID:29186559 | Free, Available for download, Freely available | SCR_017400 | 2026-09-05 06:28:23 | 2 | |||||||||
|
PILER Resource Report Resource Website 10+ mentions |
PILER (RRID:SCR_017333) | data analysis software, data processing software, software application, software resource | Software tool for analyzing repetitive DNA found in genome sequences. Software package for identification and classification of genomic repeats. Used for identifying patterns of local alignments induced by certain classes of repeats. | analysis, repetitive, DNA, genome, sequence, classification, alignment | is listed by: OMICtools | PMID:15961452 | Free, Available for download, Freely available | https://omictools.com/piler-tool | SCR_017333 | 2026-09-05 06:28:22 | 15 | ||||||||
|
3D Genome Resource Report Resource Website 10+ mentions |
3D Genome (RRID:SCR_017525) | service resource | Genome Browser for study of 3D genome organization and gene regulation and data visualization. Used to visualizing chromatin interaction data, browse other omics data such as ChIP-Seq or RNA-Seq for same genomic region, and gain complete view of both regulatory landscape and 3D genome structure for any given gene., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | 3D, genome, organization, gene, regulation, data, visualization, chromatin, interaction, omic, ChIPseq, RNAseq, regulatory, structure |
is related to: Encode has parent organization: Pennsylvania State University |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017525 | 2026-09-05 06:28:25 | 20 | ||||||||||
|
MCScan Resource Report Resource Website 10+ mentions |
MCScan (RRID:SCR_017650) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software package to simultaneously scan multiple genomes to identify homologous chromosomal regions and subsequently align these regions using genes as anchors.Used to identify conserved gene arrays both within same genome and across different genomes. Command line program to wrap dagchainer and combine pairwise results into multi alignments in column format. | Simultaneously, scan, multiple, genome, identify, homologous, chromosomal, region, align, gene, anchor, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Georgia; Georgia; USA |
Free, Available for downoad, Freely available | biotools:MCScan | http://chibba.agtec.uga.edu/duplication/mcscan/, https://bio.tools/MCScan | SCR_017650 | Multiple Collinearity Scan | 2026-09-05 06:28:27 | 42 | |||||||
|
Blobtools Resource Report Resource Website 100+ mentions |
Blobtools (RRID:SCR_017618) | data analytics software, data processing software, data visualization software, software application, software resource | Software tool as modular command line solution for visualisation, quality control and taxonomic partitioning of genome datasets. Used for interrogation of genome assemblies. Assists in primary partitioning of data, leading to improved assemblies, and screening of final assemblies for potential contaminants. | Modular, command, line, solution, visualisation, quality, control, taxonomic, partitioning, genome, dataset, genome assembly, screening, contaminant, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: BlobTools2 |
BBSRC ; James Hutton Institute/Edinburgh University School of Biological Sciences fellowship |
DOI:10.12688/f1000research.12232.1 | Free, Available for download, Freely available | biotools:blobtools | https://github.com/DRL/blobtools, https://bio.tools/blobtools | SCR_017618 | BlobTools | 2026-09-05 06:28:27 | 225 | |||||
|
Ngmlr Resource Report Resource Website 10+ mentions |
Ngmlr (RRID:SCR_017620) | NGMLR | alignment software, data processing software, image analysis software, software application, software resource | Software tool as long read mapper designed to align PacBio or Oxford Nanopore reads to reference genome and optimized for structural variation detection. | Long, read, mapper, align, PacBio, Oxford Nanopore, read, reference, genome, structural, variantion, detection, bio.tools |
is listed by: bio.tools is listed by: Debian |
National Science Foundation ; NHGRI R01 HG006677; NHGRI UM1 HG008898 |
PMID:29713083 | Free, Available for download, Freely available | biotools:ngmlr | https://bio.tools/ngmlr | SCR_017620 | coNvex Gap-cost alignMent for Long Reads | 2026-09-05 06:28:27 | 36 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the dkNET Resources search. From here you can search through a compilation of resources used by dkNET and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that dkNET has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on dkNET then you can log in from here to get additional features in dkNET such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into dkNET you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
Email: info_at_ dknet.org
